The 28-year-old, named as Lauri Love from Suffolk, was arrested by officers from the National Crime Agency (NCA) under the Computer Misuse Act after he was indicted by a grand jury in Newark, New Jersey, where it is claimed he used a server. He has been released on police bail until next February.
He also faces federal charges in Virginia for other alleged intrusions.
The US said the purpose was “to disrupt the operations and infrastructure” of the federal government.
NCA spokesman Andy Archibald said: “This arrest is the culmination of close joint working by the NCA, Police Scotland and our international partners.
“Cyber-criminals should be aware that no matter where in the world you commit cyber crime, even from remote places, you can and will be identified and held accountable for your actions.
“The NCA has well-developed law enforcement alliances globally and we will pursue and deal robustly with cyber-criminals.”
Under the Computer Misuse Act, individuals can be arrested for launching attacks from within the UK against computers anywhere in the world.
Love is believed to have lived in the Stradishall and Lowestoft areas of Suffolk.
It is alleged Love and co-conspirators in Australia and Sweden stole information about government employees, including military service members, since at least October last year by hacking into government networks and leaving behind “back doors” through which they could return to get data.
Neither of his co-conspirators have been charged in connection with the hacking.
An indictment served in a US court included pieces of instant message conversations that Love allegedly had with his partners.
In one, he is said to have written: “Ahaha, we owning lots of nasa sites.” In another exchange, he said “This ... stuff is really sensitive”, according to prosecutors.